Question: FastQC job just keeps running without any output
0
gravatar for jkoral
12 days ago by
jkoral100
United States
jkoral100 wrote:

I just installed the latest Galaxy version 18.01 of Galaxy on a virtual machine running Ubuntu. For some reason when I run FastQC, the status show FastQC on data 1: RawData and FastQC on data 1: Webpage are just spinning saying "This job is currently running". It never finishes. The version of FastQC is 0.11.6.

I am using Ubuntu server, do I need X11 or something else installed to produce the graphics for the output?

Thanks for any help you can provide.

ADD COMMENTlink modified 11 days ago • written 12 days ago by jkoral100
0
gravatar for Jennifer Hillman Jackson
12 days ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

If the job is yellow, then it is still executing. You could check your server logs to make sure it actually running. Or, try running a very small dataset through the tool as a test. If that smaller test fails or never completes and you cannot determine the problem, ask the developers directly for configuration help at Gitter: https://gitter.im/galaxyproject/Lobby or through the galaxy-dev@lists.galaxyproject.org mailing list https://galaxyproject.org/mailing-lists/.

All HTML display will be blocked by default. Add the tool to the admin whitelist to permit display. Note that the tool/job must complete before results can be reviewed in the web host. Admin > Tool Management > Manage whitelist

Admin docs: https://docs.galaxyproject.org/en/master/index.html

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 12 days ago • written 12 days ago by Jennifer Hillman Jackson24k
0
gravatar for jkoral
11 days ago by
jkoral100
United States
jkoral100 wrote:

The problem is, I can run this exact job on another instance, just not this one. It just keep spinning.I added the tool to the whitelist, but it still not produce the results. Thanks.

ADD COMMENTlink written 11 days ago by jkoral100

By "spinning", do you mean that the job is still executing (yellow in color)?

The whitelist change will not take effect until the job completes and is successful (green in color, contains output), as this only impacts the ability to view the final HTML result in the Galaxy application GUI.

Items to consider:

  1. The job is still processing. You can review the server/cluster logs on your instance to check.
  2. More resources need to be added to the instance to process jobs quicker.
  3. The job was for some reason disconnected. If you restarted your server, or using a cluster, this can occur. You might try rerunning to see if that helps.
  4. Test to see if other tools execute (to eliminate server configuration problems for being a factor).
  5. Test if this tool will run on a smaller sample of data.

If you need more configuration troubleshooting help after testing the above and reviewing the admin config docs, please use the Gitter chat to get feedback from the developers.

ADD REPLYlink written 11 days ago by Jennifer Hillman Jackson24k
0
gravatar for jkoral
11 days ago by
jkoral100
United States
jkoral100 wrote:

I was able to figure it out. Since I installed Ubuntu Server with no graphics, it would not display the results. I installed xauth xorg and xorg-dev and the job ran in about 5 seconds and displayed the output.

Thanks again for the quick replies.

Joe

ADD COMMENTlink written 11 days ago by jkoral100

Great, thanks for posting back your solution!

ADD REPLYlink modified 11 days ago • written 11 days ago by Jennifer Hillman Jackson24k
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